Where do you put header.php and footer.php?

[eluser]The Beginner[/eluser]
So does that mean that the css file I use for my menu that is currently included in my header_view could be loaded in that file instead, keeping all those things in one place? And if that is the case, obivously it would be available to header_view when it loaded?
If I understand that correctly that is really cool. I still am having difficulty getting pea brain around that. Someone used the term AutoMagically, referring to CI, that is the way I feel about it right now.lol Hopefully someday soon I will get my head around it.
Thanks,
Del